mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999228 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr16:1538464C>TN/A show variant in all transcripts IGV

HGNC symbol

PTX4

Ensembl transcript ID

ENST00000293922

Genbank transcript ID

NM_001013658

UniProt peptide

Q96A99

alteration type

single base exchange

alteration region

CDS

DNA changes

c.5G>A
cDNA.5G>A
g.519G>A

AA changes

G2E Score: 98 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs2745103

database	homozygous (T/T)	heterozygous	allele carriers
1000G	210	871	1081
ExAC	3980	21387	25367

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.535	0
	0.536	0.003
(flanking)	0.105	0.004

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	516	wt: 0.9532 / mu: 0.9560 (marginal change - not scored)	wt: TGTCATGGGGAGTGG mu: TGTCATGGAGAGTGG	TCAT\|gggg
Donor increased	511	wt: 0.80 / mu: 0.91	wt: GGTAGTGTCATGGGG mu: GGTAGTGTCATGGAG	TAGT\|gtca
Donor increased	523	wt: 0.47 / mu: 0.63	wt: GGGAGTGGAAACTGG mu: GAGAGTGGAAACTGG	GAGT\|ggaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

no alignment

ENSPTRG00000007595

n/a

Mmulatta

no alignment

ENSMMUG00000007049

n/a

Fcatus

no alignment

ENSFCAG00000010651

n/a

Mmusculus

no alignment

ENSMUSG00000044172

n/a

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000038072

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000009128

n/a

protein features

start (aa)	end (aa)	feature	details
1	25	SIGNAL	Potential.	lost
67	67	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
91	91	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
271	469	DOMAIN	Pentaxin.	might get lost (downstream of altered splice site)
300	300	DISULFID	By similarity.	might get lost (downstream of altered splice site)
323	323	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
364	364	DISULFID	By similarity.	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
406	406	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)
407	407	METAL	Calcium 1; via carbonyl oxygen (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 2 (By similarity).	might get lost (downstream of altered splice site)
408	408	METAL	Calcium 1 (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1422 / 1422

position (AA) of stopcodon in wt / mu AA sequence

474 / 474

position of stopcodon in wt / mu cDNA

1422 / 1422

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

1 / 1

chromosome

strand

-1

last intron/exon boundary

782

theoretical NMD boundary in CDS

731

length of CDS

1422

coding sequence (CDS) position

cDNA position
(for ins/del: last normal base / first normal base)

gDNA position
(for ins/del: last normal base / first normal base)

519

chromosomal position
(for ins/del: last normal base / first normal base)

1538464

original gDNA sequence snippet

GGGGCCGGGTAGTGTCATGGGGAGTGGAAACTGGGAGGTCA

altered gDNA sequence snippet

GGGGCCGGGTAGTGTCATGGAGAGTGGAAACTGGGAGGTCA

original cDNA sequence snippet

ATGGGGAGTGGAAACTGGGAGGTCA

altered cDNA sequence snippet

ATGGAGAGTGGAAACTGGGAGGTCA

wildtype AA sequence

MGSGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTRNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*

mutated AA sequence

MESGNWEVTG PPCGSRCERP PGLPRGVHGQ FRSAVGLSGL RWFRRFQEVT WTHLQNIASN
YNVSYNVDVR FRSLAEESQA VAQAVNRSQA SVQGELAQLK AWVRKLQRRG RKVDTRLRAL
DLTLGERSQQ RARERKAHKA QRDALQDSLA RLEGLVHSQG ARLAALEGRL PVAHPGTAAL
GPALVPTPTQ PEELGPTSLK LQRDRQELRA ASEHRGPPQD SSAPLQGRRE PPASGSHRVL
SGTAPKDPRQ QAWSPQVPGE ICGVGPTLVF PNASTRNVVF LSPGFVTALR ALSFCSWVRT
ASGRLGTLLS YATEDNDNKL VLHGRDSLLP GSIHFVIGDP AFRELPLQLL LDGQWHHICV
IWTSTQGRYW LHVDRRLVAT GSRFREGYEI PPGGSLVLGQ EQDSVGGGFD SSEAFVGSMS
GLAIWDRALV PGEVANLAIG KEFPTGAILT LANAALAGGF VQGANCTCLE RCP*

speed

0.49 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project